On the complexity of deriving position specific score matrices from examples

Tatsuya Akutsu, Hideo Bannai, Satoru Miyano, Sascha Ott

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Citations (Scopus)

Abstract

PSSMs (Position-Specific Score Matrices) have been applied to various problems in Bioinformatics. We study the following problem: given positive examples (sequences) andnegative examples (sequences), finda PSSM which correctly discriminates between positive andnegative examples. We prove that this problem is solvedin polynomial time if the size of a PSSM is bounded by a constant. On the other hand, we prove that this problem is NP-hard if the size is not bounded. We also prove similar results on deriving a mixture of PSSMs.

Original languageEnglish
Title of host publicationCombinatorial Pattern Matching - 13th Annual Symposium, CPM 2002, Proceedings
EditorsAlberto Apostolico, Masayuki Takeda
PublisherSpringer Verlag
Pages168-177
Number of pages10
ISBN (Electronic)9783540438625
Publication statusPublished - Jan 1 2002
Externally publishedYes
Event13th Annual Symposium on Combinatorial Pattern Matching, CPM 2002 - Fukuoka, Japan
Duration: Jul 3 2002Jul 5 2002

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume2373
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other13th Annual Symposium on Combinatorial Pattern Matching, CPM 2002
CountryJapan
CityFukuoka
Period7/3/027/5/02

Fingerprint

Bioinformatics
Computational complexity
Polynomial time
NP-complete problem
Polynomials

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Akutsu, T., Bannai, H., Miyano, S., & Ott, S. (2002). On the complexity of deriving position specific score matrices from examples. In A. Apostolico, & M. Takeda (Eds.), Combinatorial Pattern Matching - 13th Annual Symposium, CPM 2002, Proceedings (pp. 168-177). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2373). Springer Verlag.

On the complexity of deriving position specific score matrices from examples. / Akutsu, Tatsuya; Bannai, Hideo; Miyano, Satoru; Ott, Sascha.

Combinatorial Pattern Matching - 13th Annual Symposium, CPM 2002, Proceedings. ed. / Alberto Apostolico; Masayuki Takeda. Springer Verlag, 2002. p. 168-177 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2373).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Akutsu, T, Bannai, H, Miyano, S & Ott, S 2002, On the complexity of deriving position specific score matrices from examples. in A Apostolico & M Takeda (eds), Combinatorial Pattern Matching - 13th Annual Symposium, CPM 2002, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 2373, Springer Verlag, pp. 168-177, 13th Annual Symposium on Combinatorial Pattern Matching, CPM 2002, Fukuoka, Japan, 7/3/02.
Akutsu T, Bannai H, Miyano S, Ott S. On the complexity of deriving position specific score matrices from examples. In Apostolico A, Takeda M, editors, Combinatorial Pattern Matching - 13th Annual Symposium, CPM 2002, Proceedings. Springer Verlag. 2002. p. 168-177. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
Akutsu, Tatsuya ; Bannai, Hideo ; Miyano, Satoru ; Ott, Sascha. / On the complexity of deriving position specific score matrices from examples. Combinatorial Pattern Matching - 13th Annual Symposium, CPM 2002, Proceedings. editor / Alberto Apostolico ; Masayuki Takeda. Springer Verlag, 2002. pp. 168-177 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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